8TC5

Cryo-EM Structure of Spike Glycoprotein from Civet Coronavirus SZ3 in Closed Conformation

PDB DOI: https://doi.org/10.2210/pdb8TC5/pdb
EM Map EMD-41152: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Civet SARS CoV SZ3/2003
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2023-06-29 Released: 2024-05-15
Deposition Author(s): Bostina, M., Hills, F.R., Eruera, A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.11 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM reveals variation in structural motifs within animal SARS-related coronavirus spike proteins

Bostina, M., Hills, F.R., Eruera, A.

To be published.

Macromolecule Content

Total Structure Weight: 395.09 kDa
Atom Count: 27,060
Modelled Residue Count: 3,261
Deposited Residue Count: 3,318
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,106	Civet SARS CoV SZ3/2003	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F, I [auth 5], IA [auth f], D, E, F, I [auth 5], IA [auth f], L [auth I], W [auth T]	2		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain F Focus chain I [auth 5] Focus chain IA [auth f] Focus chain L [auth I] Focus chain W [auth T] Interactions & Density Focus chain D Focus chain E Focus chain F Focus chain I [auth 5] Focus chain IA [auth f] Focus chain L [auth I] Focus chain W [auth T]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth Y], EA [auth b], FA [auth c], G [auth p], H [auth 2], BA [auth Y], EA [auth b], FA [auth c], G [auth p], H [auth 2], LA [auth i], NA [auth k], P [auth M], S [auth P], T [auth Q], Z [auth W]	3		N-Glycosylation	Interactions Focus chain BA [auth Y] Focus chain EA [auth b] Focus chain FA [auth c] Focus chain G [auth p] Focus chain H [auth 2] Focus chain LA [auth i] Focus chain NA [auth k] Focus chain P [auth M] Focus chain S [auth P] Focus chain T [auth Q] Focus chain Z [auth W] Interactions & Density Focus chain BA [auth Y] Focus chain EA [auth b] Focus chain FA [auth c] Focus chain G [auth p] Focus chain H [auth 2] Focus chain LA [auth i] Focus chain NA [auth k] Focus chain P [auth M] Focus chain S [auth P] Focus chain T [auth Q] Focus chain Z [auth W]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth a], GA [auth d], J [auth G], JA [auth g], M [auth J], DA [auth a], GA [auth d], J [auth G], JA [auth g], M [auth J], PA [auth m], R [auth O], U [auth R], X [auth U]	4		N-Glycosylation	Interactions Focus chain DA [auth a] Focus chain GA [auth d] Focus chain J [auth G] Focus chain JA [auth g] Focus chain M [auth J] Focus chain PA [auth m] Focus chain R [auth O] Focus chain U [auth R] Focus chain X [auth U] Interactions & Density Focus chain DA [auth a] Focus chain GA [auth d] Focus chain J [auth G] Focus chain JA [auth g] Focus chain M [auth J] Focus chain PA [auth m] Focus chain R [auth O] Focus chain U [auth R] Focus chain X [auth U]
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth X], HA [auth e], K [auth H], MA [auth j], O [auth L], AA [auth X], HA [auth e], K [auth H], MA [auth j], O [auth L], V [auth S]	3		N-Glycosylation	Interactions Focus chain AA [auth X] Focus chain HA [auth e] Focus chain K [auth H] Focus chain MA [auth j] Focus chain O [auth L] Focus chain V [auth S] Interactions & Density Focus chain AA [auth X] Focus chain HA [auth e] Focus chain K [auth H] Focus chain MA [auth j] Focus chain O [auth L] Focus chain V [auth S]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth Z], KA [auth h], N [auth K], OA [auth l], Q [auth N], CA [auth Z], KA [auth h], N [auth K], OA [auth l], Q [auth N], Y [auth V]	5		N-Glycosylation	Interactions Focus chain CA [auth Z] Focus chain KA [auth h] Focus chain N [auth K] Focus chain OA [auth l] Focus chain Q [auth N] Focus chain Y [auth V] Interactions & Density Focus chain CA [auth Z] Focus chain KA [auth h] Focus chain N [auth K] Focus chain OA [auth l] Focus chain Q [auth N] Focus chain Y [auth V]
Glycosylation Resources
GlyTouCan: G00395TQ GlyCosmos: G00395TQ GlyGen: G00395TQ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EIC Query on EIC Download Ideal Coordinates CCD File SDF format, chain RA [auth A] SDF format, chain VA [auth B] SDF format, chain YA [auth B] MOL2 format, chain RA [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain YA [auth B]	RA [auth A], VA [auth B], YA [auth B]	LINOLEIC ACID C₁₈ H₃₂ O₂ OYHQOLUKZRVURQ-HZJYTTRNSA-N		Interactions Focus chain RA [auth A] Focus chain VA [auth B] Focus chain YA [auth B] Interactions & Density Focus chain RA [auth A] Focus chain VA [auth B] Focus chain YA [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain QA [auth A] SDF format, chain SA [auth A] SDF format, chain TA [auth A] SDF format, chain UA [auth B] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain QA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain ZA [auth C]	AB [auth C] BB [auth C] QA [auth A] SA [auth A] TA [auth A] AB [auth C], BB [auth C], QA [auth A], SA [auth A], TA [auth A], UA [auth B], WA [auth B], XA [auth B], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain QA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain QA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain ZA [auth C]